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DCF_202004_Release 1587963803 #1443

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DCF_202004_Release 1587963803 #1443

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f7f9876
copying manifests/fence/fence-config-public.yaml to nci-crdc.datacomm…
themarcelor Apr 27, 2020
b4ba397
copying manifest.json to nci-crdc.datacommons.io
themarcelor Apr 27, 2020
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140 changes: 116 additions & 24 deletions nci-crdc.datacommons.io/manifest.json
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Original file line number Diff line number Diff line change
@@ -1,23 +1,29 @@
{
"notes": [
"DCF Production Manifest. Clients hit endpoints in fence and indexd. ",
"Other services are left running to showcase the front-end."
"This is the DCF Staging env. It uses GDC's NIH Login node as IDP but instead of ",
"syncing authz information from dbGap, there is a manual whitelist. ",
"Environment is configured for Google data access methods including service account ",
"registration. Data is in multiple Google buckets with both public and *controlled* ",
"data. The controlled data is actually just public data so there's no sensitive ",
"data in this env."
],
"jenkins": {
"autodeploy": "yes"
},
"versions": {
"fence": "quay.io/cdis/fence:2020.03",
"arborist": "quay.io/cdis/arborist:2020.03",
"google-sa-validation": "placeholder:2020.03",
"indexd": "quay.io/cdis/indexd:2020.03",
"peregrine": "quay.io/cdis/peregrine:2020.03",
"pidgin": "quay.io/cdis/pidgin:2020.03",
"revproxy": "quay.io/cdis/nginx:1.17.6-ctds-1.0.1",
"sheepdog": "quay.io/cdis/sheepdog:2020.03",
"portal": "quay.io/cdis/data-portal:2020.03",
"fence": "quay.io/cdis/fence:2020.04",
"arborist": "quay.io/cdis/arborist:2020.04",
"google-sa-validation": "placeholder:2020.04",
"indexd": "quay.io/cdis/indexd:2020.04",
"peregrine": "quay.io/cdis/peregrine:2020.04",
"pidgin": "quay.io/cdis/pidgin:2020.04",
"revproxy": "quay.io/cdis/nginx:2020.04",
"sheepdog": "quay.io/cdis/sheepdog:2020.04",
"portal": "quay.io/cdis/data-portal:2020.04",
"sower": "quay.io/cdis/sower:2020.04",
"fluentd": "fluent/fluentd-kubernetes-daemonset:v1.2-debian-cloudwatch",
"jupyterhub": "quay.io/occ_data/jupyterhub:2020.03"
"jupyterhub": "quay.io/occ_data/jupyterhub:2020.04",
"metadata": "quay.io/cdis/metadata-service:v1.3.0"
},
"arborist": {
"deployment_version": "2"
Expand All @@ -34,16 +40,96 @@
"jupyterhub": {
"enabled": "no"
},
"sower": [
{
"name": "manifest-indexing",
"action": "index-object-manifest",
"container": {
"name": "job-task",
"image": "quay.io/cdis/manifest-indexing:2020.04",
"pull_policy": "Always",
"env": [
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
}
],
"volumeMounts": [
{
"name": "manifest-indexing-creds-volume",
"readOnly": true,
"mountPath": "/manifest-indexing-creds.json",
"subPath": "config.json"
}
],
"cpu-limit": "1",
"memory-limit": "1Gi"
},
"volumes": [
{
"name": "manifest-indexing-creds-volume",
"secret": {
"secretName": "manifestindexing-g3auto"
}
}
],
"restart_policy": "Never"
},
{
"name": "indexd-manifest",
"action": "download-indexd-manifest",
"container": {
"name": "job-task",
"image": "quay.io/cdis/download-indexd-manifest:1.0.1",
"pull_policy": "Always",
"env": [
{
"name": "GEN3_HOSTNAME",
"valueFrom": {
"configMapKeyRef": {
"name": "manifest-global",
"key": "hostname"
}
}
}
],
"volumeMounts": [
{
"name": "manifest-indexing-creds-volume",
"readOnly": true,
"mountPath": "/manifest-indexing-creds.json",
"subPath": "config.json"
}
],
"cpu-limit": "1",
"memory-limit": "1Gi"
},
"volumes": [
{
"name": "manifest-indexing-creds-volume",
"secret": {
"secretName": "manifestindexing-g3auto"
}
}
],
"restart_policy": "Never"
}
],
"global": {
"environment": "dcfprod",
"hostname": "nci-crdc.datacommons.io",
"revproxy_arn": "arn:aws:acm:us-east-1:584476192960:certificate/4173b316-0510-4216-8043-3f9234570475",
"environment": "dcf-staging",
"hostname": "nci-crdc-staging.datacommons.io",
"revproxy_arn": "arn:aws:acm:us-east-1:584476192960:certificate/b1f41138-54c0-4d5f-b2f3-7c5ebb20b555",
"dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json",
"portal_app": "dev",
"kube_bucket": "kube-dcfprod-gen3",
"logs_bucket": "logs-dcfprod-gen3",
"kube_bucket": "kube-dcf-staging-gen3",
"logs_bucket": "logs-dcf-staging-gen3",
"sync_from_dbgap": "True",
"useryaml_s3path": "s3://cdis-gen3-users/ncicrdc/user.yaml"
"useryaml_s3path": "s3://cdis-gen3-users/dcfstaging-users/user.yaml"
},
"canary": {
"default": 0
Expand All @@ -57,26 +143,32 @@
},
"fence": {
"strategy": "auto",
"min": 5,
"max": 15,
"min": 2,
"max": 4,
"targetCpu": 40
},
"presigned-url-fence": {
"strategy": "auto",
"min": 20,
"max": 25,
"min": 2,
"max": 10,
"targetCpu": 40
},
"indexd": {
"strategy": "auto",
"min": 2,
"max": 6,
"max": 4,
"targetCpu": 40
},
"revproxy": {
"strategy": "auto",
"min": 2,
"max": 10,
"max": 6,
"targetCpu": 40
},
"metadata": {
"strategy": "auto",
"min": 2,
"max": 5,
"targetCpu": 40
}
}
Expand Down
89 changes: 7 additions & 82 deletions nci-crdc.datacommons.io/manifests/fence/fence-config-public.yaml
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Original file line number Diff line number Diff line change
@@ -1,89 +1,14 @@
S3_BUCKETS:
tcga-protected-dcf-databucket-gen3:
cred: 'fence_bot'
tcga-public-dcf-databucket-gen3:
cred: 'fence_bot'
target-controlled:
cred: 'fence_bot'
tcga-open:
cred: 'fence_bot'
tcga-controlled:
cred: 'fence_bot'
pdcdatastore:
cred: 'fence_bot'
gdc-beataml1.0-crenolanib-phs001628-controlled:
cred: 'fence_bot'
gdc-ccle-controlled:
cred: 'fence_bot'
gdc-cgci-blgsp-phs000235-controlled:
cred: 'fence_bot'
gdc-cptac-phs001287-controlled:
cred: 'fence_bot'
gdc-ctsp-phs001175-controlled:
cred: 'fence_bot'
gdc-fm-ad-phs001179-controlled:
cred: 'fence_bot'
gdc-hcmi-cmdc-phs001486-controlled:
cred: 'fence_bot'
gdc-mmrf-commpass-phs000748-controlled:
cred: 'fence_bot'
gdc-nciccr-phs001444-controlled:
cred: 'fence_bot'
gdc-organoid-pancreatic-phs001611-controlled:
cred: 'fence_bot'
gdc-varepop-apollo-phs001374-controlled:
cred: 'fence_bot'
nci-cbiit-caninedatacommons-file:
cred: 'fence_bot'
gdc-cptac-2-phs000892-controlled:
cred: 'fence_bot'
gdc-genie-phs001337-controlled:
cred: 'fence_bot'
cds-54-phs000178:
cred: 'fence_bot'
cds-211-phs001713:
cred: 'fence_bot'
cds-207-phs001787:
cred: 'fence_bot'
cds-212-phs001437:
cred: 'fence_bot'
gdc-target-phs000218-2-open:
cred: 'fence_bot'
gdc-nciccr-phs001444-2-open:
cred: 'fence_bot'
gdc-beataml1-cohort-phs001657-2-open:
cred: 'fence_bot'
gdc-beataml1.0-crenolanib-phs001628-2-open:
cred: 'fence_bot'
gdc-cgci-blgsp-phs000235-2-open:
cred: 'fence_bot'
gdc-cptac-2-phs000892-2-open:
cred: 'fence_bot'
gdc-cptac-phs001287-2-open:
cred: 'fence_bot'
gdc-ctsp-phs001175-2-open:
cred: 'fence_bot'
gdc-fm-ad-phs001179-2-open:
cred: 'fence_bot'
gdc-genie-phs001337-2-open:
cred: 'fence_bot'
gdc-hcmi-cmdc-phs001486-2-open:
cred: 'fence_bot'
gdc-mmrf-commpass-phs000748-2-open:
cred: 'fence_bot'
gdc-nciccr-phs001444-2-open:
cred: 'fence_bot'
gdc-ohsu-cnl-phs001799-2-open:
cred: 'fence_bot'
gdc-organoid-pancreatic-phs001611-2-open:
cred: 'fence_bot'
gdc-varepop-apollo-phs001374-2-open:
cred: 'fence_bot'
gdc-ccle-2-open:
tcga-protected-dcf-databucket-gen3:
cred: 'fence_bot'
sddp-phs001554:
tcga-public-dcf-databucket-gen3:
cred: 'fence_bot'
cds-225-phs001859:
pdcdatastore-controlled:
cred: 'fence_bot'
cds-223-phs001926:
region: 'us-east-1'
dev-testing-bucketfor-matchdata:
cred: 'fence_bot'
region: 'us-east-1'